Preprint Article Version 2 Preserved in Portico This version is not peer-reviewed

Understanding UCEs: A Comprehensive Primer on Using Ultraconserved Elements for Arthropod Phylogenomics

Version 1 : Received: 30 May 2019 / Approved: 31 May 2019 / Online: 31 May 2019 (10:27:44 CEST)
Version 2 : Received: 2 August 2019 / Approved: 4 August 2019 / Online: 4 August 2019 (16:54:42 CEST)

A peer-reviewed article of this Preprint also exists.


Targeted enrichment of ultraconserved elements (UCE) has emerged as a promising tool for inferring evolutionary history in many taxa, with utility ranging from phylogenetic and phylogeographic questions at deep time scales to population level studies at shallow time scales. However, the methodology can be daunting for beginners. Our goal is to introduce UCE phylogenomics to a wider audience by summarizing recent advances in arthropod research, and to familiarize readers with background theory and steps involved. We define terminology used in association with the UCE approach, evaluate current laboratory and bioinformatic methods and limitations, and, finally, provide a roadmap of steps in the UCE pipeline to assist phylogeneticists in making informed decisions as they employ this powerful tool. By facilitating increased adoption of UCE in phylogenomics studies that deepen our comprehension of the function of these markers across widely divergent taxa, we aim to ultimately improve understanding of the arthropod tree of life.


Arachnida; insect; phylogenomics methods; target enrichment; ultraconserved elements


Biology and Life Sciences, Insect Science

Comments (1)

Comment 1
Received: 4 August 2019
Commenter: Yuanmeng Zhang
Commenter's Conflict of Interests: Author
Comment: Expanded sections on probe design and phylogenomics methods, and included metanalysis of published studies.
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